chore(agent): track .agent/ planning tree in git

Remove the blanket .agent/ gitignore so the phase roadmap, user
stories, reports, and PLAN.md are versioned with the code. Only
runtime artifacts (.agent/phase-sessions/, .agent/pipeline.log)
remain ignored. Update AGENTS.md git protocol rule to match.

.agent/user_stories/thinking-display.md

@@ -0,0 +1,103 @@
+# Story: Thinking Display
+
+**Phase:** `17_thinking_display` · **E2E:** `tests/e2e/test_thinking_display.py`
+
+## Narrative
+
+As **a user**, my local reasoning model *thinks* before it answers — and
+today those 10–30 seconds are pure silence. I want to *see* Brain think:
+its reasoning streaming live, tucked away once the answer starts — so long
+turns feel transparent instead of frozen.
+
+- **Given** I submit a question the model reasons about
+- **When** the turn streams reasoning ahead of (or around) the answer
+- **Then** a collapsible "Thinking" block streams open above the answer
+  bubble, auto-collapses on the first answer token, and stays
+  user-toggleable afterwards — while turns that emit no reasoning render
+  exactly as before.
+
+## Acceptance criteria
+1. Turns whose model stream carries reasoning show a "Thinking" block
+   (collapsible, above the answer bubble) that streams open and
+   auto-collapses on the first answer token; always user-toggleable
+   afterwards.
+2. Turns without reasoning render exactly as before (no block, no layout
+   shift).
+3. Thinking-without-answer (reasoning exhausted the token budget) shows
+   the existing empty-answer fallback with the thinking block preserved.
+4. Thinking persists with the message (phase 14) and restores collapsed
+   after reload; "New chat" clears it with everything else.
+5. Deflected turns show the amber bubble + "Maybe try" chips alongside the
+   thinking block (honesty gate untouched).
+6. A stream that dies mid-thinking/mid-answer ends in the error state
+   (retry hint) — never a silent half bubble.
+7. `BOR_STREAM_THINKING=0` suppresses `thinking` events server-side (log
+   line still counts `thinking_chars`).
+
+## UI Visualization & Structure
+- **DOM contract** (built dynamically — `index.html` is unchanged): inside
+  `.msg-body`, **before** `.bubble`:
+  ```html
+  <details class="thinking" open>
+    <summary>Thinking</summary>
+    <div class="thinking-text"></div>
+  </details>
+  ```
+  The block is created **open** at the first `thinking` event and
+  auto-collapses at the first answer token; a late/interleaved `thinking`
+  event only appends to the block — it never reopens once the answer
+  started. Restored messages (phase 14) render the block **collapsed**.
+- **Styling (Phase-08 tokens):** `details.thinking` — `--surface`
+  background, 1px `--line` border, 3px `--brand-soft` left accent,
+  `--radius-sm`; `summary` — `--brand-ink` on surface (≈**8.7:1**), 0.9rem,
+  **min-height 44px** touch target, CSS chevron `▸` rotating 90° when open
+  (0.15s transform, stills under `prefers-reduced-motion`),
+  `:focus-visible` 3px `--brand` outline; `.thinking-text` — `--ink-soft`
+  on surface (≈**6.9:1**), 0.875rem/1.55, **max-height 320px** with
+  `overflow-y: auto` (long scratchpads scroll instead of pushing the
+  answer off-screen) and tightened paragraph/list margins.
+- **Accessibility:** native `<details>/<summary>` — a real,
+  keyboard-focusable control with native open/closed announcements. **No
+  live region on the scratchpad** (announcing every reasoning chunk would
+  be hostile to screen readers); the existing `#send-status` region
+  announces turn state as before.
+- **Feedback contract:** while reasoning streams, the block *is* the
+  visible "thinking" feedback (the typing dots are removed); the UI state
+  stays `thinking` (button disabled with "Thinking…", status text
+  unchanged). The 120s pre-token guard clears on the first `thinking`
+  **or** `delta` event.
+- **Stream-drop guard:** a stream that ends without a `done` event after
+  at least one thinking/delta frame settles into the error state ("The
+  stream ended before my answer finished — try again?") — never a silent
+  half bubble.
+
+## Playwright Mapping Rule
+**Test Scenario → `tests/e2e/test_thinking_display.py`** (mock LLM,
+`"think out loud"` trigger):
+1. `test_thinking_block_streams_open_then_collapses` — submit
+   `THINK_QUESTION`. Assert `details.thinking` inside the last
+   `.msg.brain` attaches within 10s (it appears at the first `thinking`
+   event); immediately after attach, assert it is open (the mock's
+   ~800-char thinking stream gives a multi-second open window — see the
+   suite's determinism note) and `.thinking-text` is non-empty; once
+   `.bubble` text is non-empty, assert the block is **closed**; at
+   settle: `.thinking-text` contains `Step 2: Check my notes`, the bubble
+   contains the mock's deterministic answer sentence, `.source-chip`
+   count ≥ 1, send button re-enabled.
+2. `test_thinking_toggle_after_done` — after a settled `THINK_QUESTION`
+   turn, the block is closed; click `summary` → `details[open]` and the
+   full thinking text is visible; click again → closed. (Real
+   keyboard-focusable control.)
+3. `test_thinking_restored_after_reload` — settle a `THINK_QUESTION`
+   turn; capture the thinking text; `page.reload()`; the restored
+   conversation contains the brain message with a **closed**
+   `details.thinking` whose `.thinking-text` matches the captured text,
+   and the answer bubble + source chips are intact (phase-14 restore
+   path).
+4. `test_no_thinking_block_without_trigger` — submit `PLAIN_QUESTION`; at
+   settle: `page.locator("details.thinking")` count is 0 (a model that
+   doesn't think renders exactly as before — no layout regression).
+5. `test_thinking_with_deflection` — submit `THINK_DEFLECT_QUESTION`; at
+   settle: the brain message has `.is-deflected`, a `.maybe-try` group
+   with chips, and a closed `details.thinking` whose text contains
+   `Step 2: Check my notes` (thinking and the honesty gate coexist).